Abstract:

Respiratory Syncytial Virus (RSV) is a major cause of bronchiolitis and pneumonia in
infants, immunocompromised and the elderly in both developed and developing countries.
Re-infections are common and G protein variability is one mechanism to overcome herd
immunity. This is illustrated by the appearance of the BA genotype with a 60 nucleotide
duplication dominating the subtype B genotypes in epidemics worldwide. To investigate
the evolution of subtype B in South Africa (SA) since 2002 the genetic variability of the G protein was analyzed in all recent strains isolated over four years (2006-2009) in SA
hospitals. Bayesian analysis revealed a replacement of all subtype B genotypes previously
identified in SA with the BA genotype since 2006, while subtype A genotypes identified in
previous years are still circulating. Compared to BA strains from other countries, the
evolutionary rate of the SA BA genotype was shown to be 2.305 x 10-3 nucleotide
substitutions/site/year and drift was evident. The most recent common ancestor (MRCA) of
the SA BA viruses was determined to date back to 1996. All SA BA isolates clustered with
the BA-IV sub genotype and the appearance of new sub-genotypes within this branch may
occur if drift continues. Sequencing of the complete G protein of selected SA strains
revealed an additional 6 nucleotide deletion. Acquisition of the 60 nucleotide duplication
appeared to have improved the fitness of this virus and more recent subtype B strains may
need to be included in experimental vaccines to evaluate their efficacy in the current
setting of evolved circulating strains.